A new battle is underway in Pakistan with its powerful military front-and-centre, but the fight is not against armed insurgents or ideological extremists - this opponent is a muscle-flexing Supreme Court.

For the first time in decades, the military's iron grip over the South Asian country has been challenged, and it remains to be seen if it will surrender any iota of its supremacy.

Supreme Court Chief Justice Iftikhar Muhammad Chaudhry has become the military's main antagonist after he warned the army to stop playing its hand in politics.

Chaudhry was removed as Pakistan's chief justice in March 2007 after taking on corruption cases against the government of then-military ruler General Pervez Musharraf. Since his reinstatement in March 2009 - backed by a movement of lawyers and the media - the judge has brazenly resumed pursuing high-profile cases against leading politicians and military figures.

"Gone are the days when stability and security of the country were defined in terms of the number of missiles and tanks."

- Iftikhar Muhammad Chaudhry

Chaudhry ordered an investigation into the former army chief Mirza Aslam Baig and Asad Durrani, former head of the Inter-Services Intelligence - the country's feared military-intelligence agency.

Baig and Durrani had been accused of buying off politicians in the early 1990s and rigging parliamentary elections. Other former generals are also under investigation for corruption-related allegations.

A 141-page verdict by the Supreme Court accused Baig and Durrani of paying off politicians. It said military couriers had delivered millions of dollars in secret state funds to opposition politicians to defeat Benazir Bhutto's Pakistan People's Party in elections.

"The general election held in the year 1990 was subjected to corruption and corrupt practices," the October 19 verdict read. Baig and Durrani "participated in the unlawful activities", it said.

After the verdict Chaudhry also began making public statements taking aim at the military's sway over the country.

"Gone are the days when stability and security of the country were defined in terms of the number of missiles and tanks as a manifestation of hard power available at the disposal of the state," Chaudhry said in a nine-page speech he earlier gave to Pakistani bureaucrats.

Military's mea culpa

Apparently in response to the Supreme Court ruling and Chaudhry's statements, Pakistan's current army chief, General Ashfaq Parvez Kayani, spoke to a gathering of senior commanders at army headquarters in Rawalpindi on November 5. He delivered a mea culpa, followed by what some have viewed as a veiled warning to the Supreme Court.

"No individual or institution has the monopoly to decide what is right or wrong in defining the ultimate national interest," the general said. "We should not be carried away by short term considerations which may have greater negative consequences in the future.

"Armed Forces draw their strength from the bedrock of the public support. National security is meaningless without it. Therefore, any effort which wittingly or unwittingly draws a wedge between the people and Armed Forces of Pakistan undermines the larger national interest. While constructive criticism is well understood, conspiracy theories based on rumours which create doubts about the very intent, are unacceptable."

Cyril Almeida - a political columnist for the English-language daily Dawn - noted the unprecedented public nature of the row, suggesting the military may be starting to worry about losing its dominance.

"In the past, warnings would be delivered privately and directly to those concerned. Now fear is leading to open-ended public statements," Almeida told Al Jazeera. "The generals are afraid because they are losing public sympathy, and they feel it undermines their authority."

Pakistan army chief Asfaq Parvez Kayani (right) [Reuters]

The public brouhaha between the leaders of two of Pakistan's most crucial institutions is underscored by wider criticism against the military that has recently emerged.

"Their (the army's) choices and conduct have hurt this country," writes Babar Sattar, a constitutional lawyer based in Islamabad. "When called to account for their actions … they must not hide behind morale of troops or projected division between the leaders."

Losing sovereignty

In May 2011, helicopters carrying US Navy Seals flew clandestinely through the night to the town of Abbottadad, a highly militarised area in Pakistan's northwest. They stormed a compound where al-Qaeda leader Osama bin Laden was hiding, and killed him only steps away from a Pakistani army facility.

The US raid created widespread resentment in Pakistan because the military failed to stop the Americans from entering Pakistani soil.

"The myth of an all-powerful army is far removed from reality," Almeida said. "The US raid revealed a weakness. Generals cater to two primary constituencies - public opinion and the army's rank and file. They've taken a hit on both these fronts."

Public criticism has exposed a growing level of dissent within the military. After a decade of protracted fighting in Pakistan's tribal areas, many soldiers are disillusioned with a war they see as dictated from outside their borders.

Pakistan joined the US offensive against Taliban fighters and al-Qaeda in 2002 and receives about US$1bna year in coalition support.

Army support for what is perceived as "America's war" has driven a wedge between the military high command and the commanded.

New era of accountability?

Since the American raid that killed bin Laden, the military has been increasingly called into question in the courts and on the streets.

Judges and lawyers are now prosecuting army officials for their alleged involvement in the disappearance of thousands of political activists, mostly in Balochistan.

Pakistan's army has been locked in a decade-long insurgency in the southern, resource-rich province.

In a report titled "Blinkered slide into chaos", the Human Rights Commission of Pakistan said there is "credible allegations of the involvement of state security forces" in cases of "enforced disappearances".

Malik Siraj Akbar, a Balochi journalist living in exile in the US, goes much further in his allegations against the military.

"The security establishment arrests, tortures and murders anyone who criticizes its policy," Akbar told Al Jazeera. "Thousands have disappeared in the province, almost all were political activists critical of the army's handling of the situation."

"People are being killed here. There are no jobs, no electricity, but the politicians are making billions."

- Awab Alvi, social activist and blogger

While the military has increasingly been scrutinised, Pakistan's politicians are also under the microscope.

People were optimistic when democracy returned with the March 2008 elections. There was hope the politicians and the chief justice would set a new course for the country, maybe even disengage with the US and end the war.

Five years later, Pakistan's economy is in ruins. Some $94bn has been lost to corruption, tax evasion and bad governance, according to Transparency International, which monitors growth in developing countries.

Awab Alvi, a blogger and organiser for Imran Khan's Pakistan Tehrik-e-Insaf party, said he doesn't like what the military does but despises what Pakistan's political elite is up to.

"People are being killed here. There are no jobs, no electricity, but the politicians are making billions," Alvi told Al Jazeera. "People don't always agree with what the army has done, but they hate what the politicians are doing."